READIT: a novel technology used in the interrogation of nucleic acid sequences for single-nucleotide polymorphisms

Analytic validity of genetic tests to identify factor V Leiden and prothrombin G20210A

The objective of this study is to systematically review methods for detecting Factor V Leiden or prothrombin G20210A. English-language literature from MEDLINE, EMBASE, The Cochrane Library, the Cumulative Index to Nursing and Allied Health Literature, PsycInfo(c), 2000-December 2008. Studies assessed methods for detection of these mutations in at least 10 human blood samples and reported concordance, discordance, or reproducibility. Two investigators abstracted data on the sample selection criteria, test operators, DNA extraction, experimental test, reference standard, commercial instruments, concordance rates, explanation of any discordance, and whether discordance resolved after repetition. We assessed strength of the evidence using the GRADE criteria. We reviewed 7,777 titles and included 66 articles. The majority of the reviewed studies used PCR-RFLP or AS-PCR as the reference standard. The studies demonstrated that commercially available and precommercial tests have high analytic validity with all having greater than 99% concordance with the reference standard. With a few exceptions, discordance resolved with repetition of the test, suggesting operator or administrative errors were responsible for the discordant results. In the quality assurance studies, greater than 98% of laboratories demonstrated high, even perfect, accuracy when asked to diagnose a sample with a known mutation. The majority of errors came from a limited number of laboratories. Although not all methods may be accurate, there is high-grade evidence that genetic tests for the detection of FVL and prothrombin G20210A have excellent analytic validity. There is high-grade evidence that most, but not all, clinical laboratories test for FVL and prothrombin G20210A accurately.

Pharmacogenomic genotyping methodologies

“Personalized medicine” based on an individual’s genetic makeup is slowly becoming a reality as pharmacogenomics moves from the research setting to the clinical laboratory. Concordance studies between genotype and phenotype have shown that inherited mutations in several key drug-metabolizing enzymes, such as cytochrome P450 (

The READIT assay as a method for genotyping NAT1*10 polymorphisms

Polymorphisms in the N-acetyltransferases (NATs) have been associated with increased risks for the development of a variety of cancers. The NAT1*10 allele, for example, has been reported to be associated with an increased risk of colon and urinary bladder cancers, among others. Therefore, considerable effort is being placed on the development of genotyping methodologies for NAT activities both for pharmacological as well as disease preventative applications. Most NAT genotyping approaches are gel based and consist of PCR-restriction fragment length polymorphism (RFLP) analysis, allele-specific PCR, or both. Although these approaches have their utility, they are slow, labor intensive, and are not amenable to automation. Recently, a novel approach to genotyping known as the READIT Assay has been introduced. The READIT methodology involves a reversal of the DNA polymerase reaction to generate dNTPs through the phosphorolytic cleavage of oligonucleotide probe molecules annealed to target DNAs. In a coupled reaction, kinase converts the resulting dNTPs to ATP. ATP production is then monitored by the addition of luciferase, generating a light signal proportional to the amount of dNTPs generated through probe depolymerization. We describe the development of a READIT genotyping protocol for the analysis of NATs using the NAT1*10 allele as a model system and demonstrate its utility for the analysis of archival dried blood specimens. We applied this technology to genotype 678 DNAs at the NAT-1088T --> A polymorphic site, and 680 DNAs for the 1095C --> A polymorphism. We report complete concordance for the 1088T --> A polymorphism for all 678 genotypes previously determined by RFLP analysis.

Evaluation of electronic microarrays for genotyping factor V, factor II, and MTHFR

BACKGROUND

Genetic risk factors associated with venous thrombosis include mutations in the factor V (Leiden), factor II (prothrombin), and methylenetetrahydrofolate reductase (MTHFR) genes. We evaluated a method using electronically addressable microarrays for the detection of mutations in these genes that have been associated with vascular disease.

METHODS

The NanoChip Molecular Biology Workstation (Nanogen) uses electronic microarrays for mutation detection. Factor V, factor II, and MTHFR genotypes identified in the NanoChip system on 225 samples were compared with genotypes from LightCycler assays (Roche). We determined within- and between-cartridge signal and ratio variation and analyzed the effect of additional mutations at or near the detection area used for the NanoChip assays.

RESULTS

Genotypes determined for all three mutations on the NanoChip platform were in complete concordance with LightCycler results. Within-cartridge signal variation as measured by the CV of fluorescence signals was <10% for each allele when present. The within-cartridge CV for heterozygous mutant/wild-type ratios was <8.5%, and between-cartridge CV was <18%. A dilution study showed that results could be obtained in this assay with 6 ng of nucleic acid per PCR, the lowest input tested. The presence of additional sequence variations near the expected mutations can produce equivocal or discrepant results.

CONCLUSIONS

Mutation detection using the NanoChip Molecular Biology Workstation was accurate and reproducible for the three assays evaluated.

Clinical utility of factor V leiden (R506Q) testing for the diagnosis and management of thromboembolic disorders

OBJECTIVE

To review the current state of the art regarding the role of the clinical laboratory in diagnostic testing for the factor V Leiden (FVL) thrombophilic mutation (and other protein C resistance disorders), and to generate, through literature reviews and opinions of recognized thought-leaders, expert consensus recommendations on methodology and diagnostic, prognostic, and management issues pertaining to clinical FVL testing.

DATA SOURCES, EXTRACTION, AND SYNTHESIS

An initial thorough review of the medical literature and of current best clinical practices by a panel of 4 experts followed by a consensus conference review, editing, and ultimate approval by the majority of a panel of 28 additional coagulation laboratory experts.

CONCLUSIONS

Consensus recommendations were generated for topics of direct clinical relevance, including (1) defining those patients (and family members) who should (and should not) be tested for FVL; (2) defining the preferred FVL laboratory testing methods; and (3) defining the therapeutic, prophylactic, and management ramifications of FVL testing in affected individuals and their family members. As FVL is currently the most common recognized familial thrombophilia, it is hoped that these recommendations will assist laboratorians and clinicians caring for patients (and families) with this common mutation.